Viruses

Viruses, viroids, and prions are all acellular pathogens. They are not within any kingdom and carry their own significant characteristics.

obligate intracellular parasite – require a host to cause damage

filterable – small enough to be filtrated

contains an outer protein coat and inner genome

has only 1 kind of nucleic acid (RNA or DNA, but never both)

lacks metabolic abilities

Viruses can be found either inside a cell (intracellular) or outside of a cell (extracellular). If it is found extracellular, the virus is called a virion. A virion contains a protein coating called a capsid, which surrounds the core of the virus containing the nucleic acid (either DNA or RNA). Together with the capsid and the DNA or RNA core is called a nucleocapsid. Some virions also contain an envelope which is made up of a phospholipid membrane. Both the capsid and the envelope are important in protection and providing shape to the virus.

mutagen – anything physical or chemical that causes mutations in an organism

reverse transcriptase – these enzymes were discovered from retrovirses and its effects on DNA. Using reverse transcriptase, scientists are able to make DNA out of RNA. These DNA are called complementary DNA or cDNA. After making cDNA from eukaryotic mRNA, scientists are able to input cDNA into the genome of the prokaryotic DNA. One main reason why this is useful is that prokaryotes are not able to excise or remove the introns (junk DNA or noncoding sequences) of DNA in eukaryotes. Since eukaryotes mRNA are already processed and had removed the introns, the newly made cDNA would also be free from introns!

Quick DNA Overview

Deoxyribosenucleic acid, as you know in humans and in other eukaryotic organisms codes our chromosomes and makes us the way we are!

Similarly, in prokaryotes, like bacteria, DNA makes up their genetic code or in other words what they are. This includes their function and their appearance.

Universally, DNA contains purines (adenosine, guanine) and pyrimidines (cysteine, thymine, uracil (found in RNA)). These guys are the bases, in which three of it together will code for a codon, that signifies an amino acid. A sequence of these codons assist with making up a peptide chain. As you know, peptides together, after having been rearranged into a 3D structure is a protein.

As you can see in the picture, DNA’s backbone is connected by phosphodiester bonds (I can get into this later and why its called what its called). These bonds help create the phosphate backbone of DNA. Since phosphate groups (PO4–) are negatively charged, a chunk of PO4– used as the backbone of the DNA will make the DNA a highly negative molecule.

As you already know, DNA is a double helix. The two strands are antiparallel. Basically, DNA strands are replicated from what is called the 5′ (five prime) end to the 3′ end (I’ll break it down in another post).

5′——-TAG———>3′

3′<—–ATC———–5′

The bases (T, A, G, C) are connected to each other by weak hydrogen bonds.

Similar to Gram stain, acid fast stain, and flagellar stain, capsule and spore stain are used to differentiate between microbes.

Capsule

Purpose: Our immune system contains neutrophils and macrophages that fight against foreign bodies or antigens. Capsules, which contains mucoid polysaccharides or polypeptides, protects bacterial cells against our immune system (macrophage and neutrophils). Capsules are also resistant to stains, hence capsule stain techniques are staining around the cell and not the cell wall or membrane directly (different from Gram and Acid fast stains).

Acidic or Negative Stain – used to stain the background

Nigrosin

Congo Red

India Ink

In this first step, there is NO heat fixing because it will cause the cells to shrink, which will give a false reading of a white halo around the cells. This may cause a misrepresentation of a capsule.

There are various ways in assessing DNA and its components. One widely used is electrophoresis, which utilizes electricity to measure the length of DNA fragments. This mechanism can be used for identification either for unknown diseases or human DNA, determining an inherited disease or finding cures for such diseases (National Health Museum).